Viral Microarray - Cultured Virus Set
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-21318E-GEOD-21317GSE21319
PROVIDER: PRJNA129469 | ENA |
REPOSITORIES: ENA
Publications
Nonparametric methods for the analysis of single-color pathogen microarrays.
Jabado Omar J OJ Conlan Sean S Quan Phenix-Lan PL Hui Jeffrey J Palacios Gustavo G Hornig Mady M Briese Thomas T Lipkin W Ian WI
BMC bioinformatics 20100628
<h4>Background</h4>The analysis of oligonucleotide microarray data in pathogen surveillance and discovery is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied.<h4>Results</h4>Positive predictive value and f ...[more]
Similar Datasets
Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with various viruses, then RNA was harvested. RNA was converted to cDNA, then amplified, labeled and hybridized to the array.
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Project description:Viral Microarray - Control Set
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Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. Overall design: A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with various viruses, then RNA was harvested. RNA was converted to cDNA, then amplified, labeled and hybridized to the array.
2010-05-24 | GSE21318 | GEO
Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with various viruses, then RNA was harvested. RNA was converted to cDNA, then amplified, labeled and hybridized to the array.
2010-05-24 | E-GEOD-21318 | ArrayExpress
Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with West Nile Virus, then RNA was harvested. RNA was converted to cDNA, then copy number was quantified by quantatative real-time PCR. RNA stocks were diluted to 10^4 or 10^6 copies per microliter then converted to cDNA, amplified, labeled and hybridized to the array. Human Lung RNA was used as a control and spiked in at 10ng or 200ng.
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Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. Overall design: A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with West Nile Virus, then RNA was harvested. RNA was converted to cDNA, then copy number was quantified by quantatative real-time PCR. RNA stocks were diluted to 10^4 or 10^6 copies per microliter then converted to cDNA, amplified, labeled and hybridized to the array. Human Lung RNA was used as a control and spiked in at 10ng or 200ng.
2010-05-24 | GSE21317 | GEO
Project description:Background: The analysis of oligonucleotide microarray data in pathogen surveillance and discovery assays is a challenging task. Target template concentration, nucleic acid integrity, and host nucleic acid composition can each have a profound effect on signal distribution. Exploratory analysis of fluorescent signal distribution in clinical samples has revealed deviations from normality, suggesting that distribution-free approaches should be applied. Results: An examination of both positive predictive value and false positive rates was employed to assess the utility of three well-established nonparametric methods for the analysis of viral array hybridization data: (1) Mann-Whitney U, (2) the Spearman correlation coefficient and (3) the chi-square test. Of the three tests, it was the chi-square that proved most useful. Conclusions: The acceptance of microarray use for routine clinical diagnostics will require that the technology be accompanied by simple yet reliable analytic methods. We report that our implementation of the chi-square test yielded a combination of low false positive rates and a high degree of predictive accuracy. A set of comprehensive probes covering vertebrate viruses was designed and printed using Agilent in-situ fabrication. Cells in tissue culture were infected with West Nile Virus, then RNA was harvested. RNA was converted to cDNA, then copy number was quantified by quantatative real-time PCR. RNA stocks were diluted to 10^4 or 10^6 copies per microliter then converted to cDNA, amplified, labeled and hybridized to the array. Human Lung RNA was used as a control and spiked in at 10ng or 200ng.
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